Commensal microbiome and gastrointestinal mucosal immunity: Harmony and conflict with our closest neighbor

Abstract Background The gastrointestinal tract contains a wide range of microorganisms that have evolved alongside the immune system of the host. The intestinal mucosa maintains balance within the intestines by utilizing the mucosal immune system, which is controlled by the complex gut mucosal immune network. Objective This review aims to comprehensively introduce current knowledge of the gut mucosal immune system, focusing on its interaction with commensal bacteria. Results The gut mucosal immune network includes gut‐associated lymphoid tissue, mucosal immune cells, cytokines, and chemokines. The connection between microbiota and the immune system occurs through the engagement of bacterial components with pattern recognition receptors found in the intestinal epithelium and antigen‐presenting cells. This interaction leads to the activation of both innate and adaptive immune responses. The interaction between the microbial community and the host is vital for maintaining the balance and health of the host's mucosal system. Conclusion The gut mucosal immune network maintains a delicate equilibrium between active immunity, which defends against infections and damaging non‐self antigens, and immunological tolerance, which allows for the presence of commensal microbiota and dietary antigens. This balance is crucial for the maintenance of intestinal health and homeostasis. Disturbance of gut homeostasis leads to enduring or severe gastrointestinal ailments, such as colorectal cancer and inflammatory bowel disease. Utilizing these factors can aid in the development of cutting‐edge mucosal vaccines that have the ability to elicit strong protective immune responses at the primary sites of pathogen invasion.

Mucosal immunity refers to the local immunity of the mucosal tissues and certain glands of the respiratory, genitourinary, and gastrointestinal tracts, which are in contact with the outside world.Its primary function is to remove pathogenic microorganisms that invade the body through the mucosal surface.The mucosal immune system operates separately from the broader immune system but is inseparable from the systemic immune system.The gastrointestinal mucosal system may have been the gateway of direct contact with external antigens, possibly linked to the need to deal with the complex and dynamic populations of commensal bacteria.
The GI tract contains a variety of bacteria, archaea, and eukaryotes, collectively termed the "gut commensal microbiome."Commensals has formed a relationship of mutually beneficial coexistence with the host over thousands of years.The microbiota that live in the GI tract help the host in many ways such as metabolic function, 1 trophic function, 2 immunologic function, 3 and intestinal defense function. 2However, host and gut commensal microbiome's homeostasis can be disrupted due to an altered microbial composition, causing intestinal and extra-intestinal diseases.
This review outlines our present knowledge of the human GI commensal microbiota and gastrointestinal mucosal immunity, a representative overview of how they interact and impact host health.

| COMMENSAL MICROBIOTA: OUR LONG-STANDING NEIGHBOR
Vertebrates and bacteria have co-evolved in intimate contact for more than 150 million years.Over 10^14 microorganisms have been found in the GI tract, which is roughly 10 times more bacterial cells than there are human cells. 4Our mucosal surfaces, therefore, involve an integration with the resident microbiota to create a "supraorganism," referring to the host, and all the microbes living inside it.
Most microbiome studies have focused on bacteria, and less attention has been paid to viruses, fungi, and archaea.However, these rare microbial components have a relatively rich composition.Fungi in the GI are highly susceptible to environmental factors, especially diet. 5The three groups that were found the most frequently were mucoromycetes (62.94%-97.56%),ascomycetes (0.89%-31.06%), and basidiomycetes (1.30%-7.63%).Euryarchaeota was the most abundant phylum for archaea, and Methanobacteriaceae was the most common family. 6iruses are lower in content than bacteria but are a stable part of the entire microbial ecosystem, among which Bacteriophages are most identified. 7

| Biogeography of commensal microbiota
Each mucosal surface has cell types and breeds different microenvironments, which result in the biogeography of microbiota.Variation of microbial habitats along the lengths of the GI tract is affected by gradients in nutrients and chemicals as well as segregated host immune activity.For instance, compared to the colon, the small intestine is more acidic, has higher quantities of oxygen, and contains more antimicrobials.Therefore, the microbiome of the small intestine is dominated by facultative anaerobes with rapid growth. 8hese communities of bacteria evolve with the host and are highly specialized in occupying different niches.From a population of 10^2-10^3 aerobic organisms/gram luminal contents in the proximal stomach and duodenum to a population of 10^11-10^12 predominantly anaerobic bacteria/gram in the cecum and colon, these microorganisms increase in both concentration and complexity as they migrate through the digestive tract, according to a molecular characterization of the microbial makeup of fecal and mucosal samples using 16 s ribosomal DNA and RNA.The four classes of bacteria known as Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria account for more than 99% of the gut microbiota. 9,10he Clostridium XIV and IV groups, which make up the majority of connected colonic species (64%), and the Bacteroidetes, which make up 23% of normal species, are the leading Firmicutes.The Enterobacteriaceae family, which includes Escherichia coli, makes up less than 10% of all symbiotic bacteria. 10Because of sampling difficulties, studies about small intestinal microbiota are rare.Streptococceae, Lactobacillales, Actinomycinae, and Corynebacteriaeceae (Bacillus subgroup of Firmicutes) were enriched, while Clostridia and Bacteroides were depleted, according to a molecular study of bacteria found in the mucosa 10 (Table 1).

| Role of commensal microbiota in health
Additionally to the function of the gut flora in immunity, which we will focus on next, they have a non-negligible impact on human health in other ways.
To participate in various metabolic processes in the human body, our microbiome joins forces with the host to form a host-microbiota co-metabolism structure.Complex carbohydrates can be fermented by bacteria to produce metabolites like SCFAs, which are essential chemical messengers between the microbiota and host.It is hypothesized that SCFA has effects that work together to enhance intestinal, hepatic, and overall glucose homeostasis. 11Microbiota metabolism also involves bile acid metabolism, 12 choline metabolism, 13 tryptophan metabolism, 14 etc.
The trophic function of the microbiota cannot be ignored either.By boosting the expression of intestinal nutrient transporters, the gut microbiota supplies nutrients to the host.SCFAs further promote the intestinal gluconeogenesis process to form supporting lipids. 15The gastrointestinal microbiota is also involved in the de novo synthesis of essential vitamins that cannot be produced by the host, such as Vitamin B12. 16Of particular note is that butyrate is a vital energy source for colonocytes. 17

| MUCOSAL IMMUNITY: THE FENCE WALL IN BETWEEN
Different inductive and effector sites make up the immune system of the gut mucosa.The inductive sites are the mesenteric lymph nodes, which have the physically compartmentalized organization typical of the peripheral lymphoid organ, and the gut-associated lymphoid tissues (GALT). 18,19

BOX
The GALT is a lymphoid tissue located in the submucosa of the intestine and comprises the Peyer's patches; isolated lymphoid follicles (ILF), which are found throughout the intestine; the esenteric lymph node (MLN); the vermiform appendix and diffuse immune cells. 18PP and ILF are connected to the MLN via lymphatic vessels, which are the sites of antigen recognition and activation of intestinal mucosal immune cells.A layer of follicleassociated epithelium (FAE) separates the lymphoid tissues from the stomach lumen.It consist of mainly intestinal epithelial cells with scattered microfold cells (M cells). 20M cells are epithelial cells with specializations, which are cytosolic transporters of antigens.They absorb chemicals and particles from the gut lumen via endocytosis or phagocytosis and transport them via membrane-bound vesicles to APC to initiate mucosal immune response-a process known as transcytosis [21][22][23][24] (Figure 1).The majority of Intraepithelial lymphocytes (IELs) can be found in the small and large intestines.90% of IELs are T cells, 80% of which are CD8+ T cells.They express chemokine receptor CCR9 and α E β 7 integrin (CD103), allowing them to bind to CCI25 and E-cadherin expressed by intestinal epithelial cells and localize to the inner intestinal epithelium.IELs are mainly divided into two categories: alEL and bIEL.alEL is primarily conventional CD8 + CTL activated by an antigen, expressing αβTCR and CD8αβ heterodimer, with a TCR of limited multiplicity.It can be directly activated by specific MHC-antigenic peptides to exert mucosal anti-infection effects like the conventional class I MHC-restricted cytotoxic T cells, killing virus-infected cells. 25bIEL is intrinsically immune lymphocytes that migrate directly from the thymus, express αβTCR, γδTCR or CD8αα homodimer, and high levels of the C-type lectin receptor NKG2D to promote barrier integrity and protective immunity. 26,27y contrast, efficacy or memory CD4 T cells predominate in lamina propria lymphocytes (LPLs).More than 95% of intestinal lamina propria T cells bear the αβ isotype of the antigen-specific T cell receptor.Recent studies show that the LP also carries a large population of heterogeneous innate lymphocytes (ILCs), including not just classical NK cells but also other cell types that can be categorized into three different groups-ILCs1, ILCs2, and ILCs3-based on cytokines and transcription factors they express.ILCs F I G U R E 1 Composition of the intestine-associated lymphoid tissue (GALT).The intestinal mucosa of the small intestine is composed of a layer of epithelial cells that digest food and absorb nutrients.The tissue beneath the epithelial cells is called the lamina propria.These tissues are located in the intestinal wall and and are protected from the contents of the intestinal lumen by the epithelium.The most prominent lymph nodes in the body are the MLN, which are connected to the PP and intestinal mucosa via the outflow lymphatics.Both PP and MLN contain T-cell areas and B-cell follicles, and the independent lymphoid follicles are mainly composed of B cells.Lymphocytes are scattered throughout the mucosal tissue and are mainly effector T cells and antibody-secreting plasma cells.Effector lymphocytes are present in the interepithelial and lamina propria layers, and lymphatic fluid drains from the lamina propria to the MLN.contribute to hosting defense against infection, metabolic homeostasis, and tissue repair. 28he overload of effector lymphocytes in the mucosal tissues, even in the absence of disease, may seem like a chronic inflammatory response and maintains the favorable relationship between the host and bacteria.

| RESPONSES TO ENTERIC PATHOGENS: COMMUNICATION IS NECESSARY FOR THE NEIGHBORHOOD
Resisting infectious agents is the primary function of the mucosal immune response, thus the host must be able to create a variety of immune responses to meet the challenge posed by certain pathogens.The innate immune system is the initial line of defense against pathogens, which is a characteristic shared by all immune responses.Thus we only emphasize characteristics that the intestine monopolizes.
The most important mechanism of innate immunity involves the epithelial cells themselves.The intestinal mucosal layer of mucus, the glycocalyx on the microvilli of absorptive intestinal epithelial cells, and the tight cell junctions between intestinal epithelial cells all work together to produce a physical barrier that is normally impenetrable to intruders. 29n the apical and basal surfaces of epithelial cells are TLRs, the first pattern-recognition receptors (PRRs) that detect pathogen-associated molecular patterns (PAMPs). 30hey are either situated on the cell membrane (TLR1, TLR2, TLR4, TLR5, TLR6, and TLR10) or inside vesicles (TLR3, TLR7, TLR8, TLR9, TLR11, and TLR13). 31Ligation of TLRs proteins stimulates cellular responses induced are mediated by several signaling molecules and cascades, incorporating the adapters MYD88 and TIR domain-containing adapter protein inducing IFNβ (TRIF).][33] Epithelial cells also express the cytosolic NOD-like receptors (NLRs) during enteric infections, which, according to their amino-terminal domain, can be divided into three major subfamilies: the NOD proteins (NOD1, NOD2, and NLRC4), the NLRP family or the NAIPs. 34The NF-B and MAPK signaling pathways are activated when NOD proteins bind to the receptor-interacting serine/threonine kinase (RICK). 34By contrast, NLR proteins form inflammasome and activate caspase 1, which cleaves pro-IL-1 and pro-IL-18. 35ecent studies recently found that another important anti-infection mechanism for epithelial cells is autophagy.In this process, a double-membrane shard in the cytoplasm termed phagophore devours various cytoplasmic contents to make an autophagosome, which coalesces with lysosomes to degrade the contents.When autophagy is disrupted, bacteria penetrate the body, and NFκB-mediated inflammation is activated.This process is promoted by NOD1 and NOD2. 36,37hen innate defenses are broken down, adaptive immune responses are induced.If pathogen penetrates the subepithelial space, it may contact TLRs on the inflammatory cells there, thus sparking the cascade of inflammatory mediators and activation of local antigenpresenting cells such as DCs.DCs will express costimulatory molecules and cytokines such as IL-1, IL-6, IL-12, and IL-23 38 and facilitate the development of effector T cells, including TH17 cells, γδ T cells, NK cells, and ILC3s to secrete IL-17 and IL-22. 39These cells amplify the host immune response by stimulating the IEL to secrete CXCchemokines attracting neutrophils. 40,41Antimicrobial peptides (AMPs) are produced in response to IL-17 and IL-22, and these AMPs alter the gastrointestinal tract's microbiota makeup. 42Similarly, IgA-producing B lymphocytes are produced in PPs and MLN, generating plasma cells that accumulate in the lamina propria to regulate gut microbes and harmful bacteria by secretory IgA (sIgA). 43hese antibodies mutually combine 44 and regulate the microbiota make-up of the digestive tract 45 to control causes and effects of inflammation 46 and defense against penetration pathogens 44 (Figure 2).

| MUCOSAL TOLERANCE: AWESOME HARMONY WE ESTABLISH
Antigens of commensal bacteria usually do not induce an inflammatory immune response.The mucosal immune system has evolved with these exogenous antigens and thus developed mechanisms to respond to innocuous antigenic substances, which is a very complicated process that involves triggering some immune responses while suppressing others.
There are shreds of evidence that the organized structures of the GALT, such as Peyer's PP and ILF, are crucial to the immune system's ability to recognize inhaled antigens on particles.The MLN has been identified as the site of oral tolerance induction because mice lacking CCR7, a critical chemokine receptor for cell migration to lymph nodes, were unable to generate oral tolerance. 47At the same time, tolerance can be developed orally without the presence of Peyer's patches. 48,491][52][53] After taking up the antigen, CD103+ DCs exhibit elevated RALDH2 levels, an enzyme metabolizing retinol into retinoic acid.Retinoic acid programs newly primed T cells to migrate to the MLN by means of gut-homing markers, such as chemokine receptor CCR9 and the integrin α4β7. 54In addition, CD103+ DCs express significant quantities of indoleamine 2,3-dioxygenase (IDO), an enzyme that catabolizes tryptophan and activates Foxp3+ Tregs. 55fter the Tregs are generated in the MLN, they migrate to the lamina propria, where they are expanded to evoke tolerance. 56][59] Antigen dosage is the key determinant of which form of peripheral tolerance develops following oral administration of antigen. 60High antigen concentrations primarily induce anergy or clonal deletion, whereas low antigen levels promote active control of suppressor cells(Tregs). 61hese two forms may occur simultaneously, but they are distinct (Figure 3).
The following criteria were used to distinguish between these two mechanisms: (i) investigations in which low dosages of an auto antigen suppress experimental autoimmune disorders by stimulating the production of regulatory cells that are suppressed through the secretion of inhibitory cytokines such as TGFβ 62 ; (ii) investigations which showed after large doses of clonal antigen anergy happen, but there's with no evidence of active suppression 63,64 ; (iii)investigations revealed transferrable suppression following mucosal tolerance, 65 including two aspects one that was abolished by treatment with low dose cyclophosphamide and one that was not.The difference was determined by the dose of the antigen 66 ; (iv) investigations of a strong contrast demonstrating the direction the two distinct mechanisms depend on the dose. 67Low versus high dose feeding regimes elicit unique mechanisms of resistance to autoimmune uveitis, according to reports. 68ow antigen dosages stimulate antigen-specific regulatory cells, which involve a presentation of antigen in the GI.Such presentation initially induces Tregs, which recognize antigens and subsequently secrete the suppressive cytokine TGFfJ.Th2 responses in the GI then promote the secretion of IL-4 and IL-IO.These antigenspecific Tregs move to lymphoid organs where they release cytokines that dampen an immune response to illness without targeting a specific antigen (bystander suppression). 68Several variables can affect the formation of regulatory T cells, such as requirements for costimulation, the cytokine environment in which the immune response is created, and the differential development of epitopes that may selectively activate certain regulatory cells are discussed.
High doses of antigen promote systemic antigen presentation after antigen transits the digestive tract and gets into the systemic circulation, which induces disability of Th1 cells, primarily via clonal anergy.Anergy is defined as a state of T cell unresponsiveness characterized by a lack of proliferation, IL-2 production, and IL-2 receptor (IL-2R) expression. 69Experimentally, anergy can be distinguished from clonal deletion by confirming the existence of antigen-specific TCR clonotypes or by releasing cells from their anergic state by preculturing them in IL-2. 70The factors determining the degree of the clonal anergy following high doses of antigen are still unknown; nevertheless, the amount of antigen passing into the systemic or portal circulation or the filtration of the gut may be the most likely impact causes.It is unknown why high concentrations of antigen result in decreased active suppression, however it may be related to the activation of cells involved in the production of active suppression.
Once oral tolerance is induced, numerous antigenspecific immune responses Th1 and Th2 are suppressed, including immunoglobulin (IgM, IgG) synthesis [71][72][73] and creation and discharge of immunoregulatory cytokines, such as TGF-β, IL-10 and IL-4. 61,73 significant conceptual advance in the study of oral tolerance is the recognition of the importance of TGF-β.It is an elementary link between different subspecies of induced Treg cells and thus is involved in the transformation of CD4 + CD25-cells into CD4 + CD25 + T cells via Foxp3. 74][77] Commensal bacteria are a potential threat, so unlike soluble food antigens, they do not induce a state of systemic immune unresponsiveness.When these pathogens infiltrate the circulation through the mucosa, they can trigger the normal main systemic immune response.

| THE MODULATING FUNCTION OF MICROBIOTA: THE IMPACT THAT NEIGHBORS BRING TO US
Possibilities for microbiota to regulate the host's physiology include the development of an incredibly wide metabolite repertoire.Colonic microbial fermentation of undigested or partially digested dietary fibers produces short-chain fatty acids (SCFAs) like butyric acid, propionic acid, and acetic acid, which are able to access through the intestinal epithelia and interact with host cells, thereby influencing immune. 78These microbiotagenerated metabolites are critical energy sources not only for the gut microbiota but also for intestinal epithelial cells (IECs) and have a variety of regulatory roles in host physiology and immunity. 79SCFAs have numerous impacts, including improved epithelial barrier function and immunological tolerance, which promote gut homeostasis via distinct mechanisms: increased mucus F I G U R E 3 The proximity of feeding antigen determines the various oral tolerance processes.
production by intestinal goblet cells 80 ; inhibition of nuclear factor-κB (NF-κB) 81,82 ; activation of inflammasomes and subsequent production of interleukin-18 (IL-18) 83 ; increased secretion of secretory IgA (sIgA) by B cells 84 ; decreased expression of T cell-activating chemicals on APCs, such as dendritic cells (DCs) 85 and macrophage 86 ; and elevated levels of regulating T (Treg) cells in the colon, including their expression of forkhead box P3 (FOXP3) 87,88 and their production of antiinflammatory cytokines such as IL-10. 89nother mechanism by which the microbiota affects the host is by triggering epigenetic changes in host cells.To achieve this, SCFAs and other microbial metabolites regulate histone acetylation.The modulation of Treg differentiation by butyrate is a powerful example of microbiota influence on the immune system via epigenetic control. 90The microbiota also causes alterations in DNA or histone methylation. 91,92ecently, researchers discovered bacterial extracellular vesicles (EVs) that elicit distinct host responses based on the specific microorganism they come from. 93Similar to LPS, the immunogenicity of microbiota-derived extracellular vesicles (EVs) varies depending on the type of microorganisms.EVs from pathogenic bacteria are linked to pro-inflammatory responses, while EVs from commensal bacteria trigger anti-inflammatory responses.For instance, electric vehicles (EVs) derived from a symbiotic strain of E. coli bacteria increased the production of mucosal cytokines that are crucial for the host's immune response. 94Although our understanding of microbiota-derived extracellular vesicles (EVs) primarily comes from studying their impact on the stomach, recent research has revealed that these EVs also play a role in regulating the immune system throughout the body.Specifically, microbiota-derived EVs prepare neutrophils to respond to secondary stimuli by triggering inflammatory reactions. 95

| Regulation of epithelial cells by the microbiota
To limit inflammation and microbial translocation, the primary strategy taken by the host is reducing microbe interaction with the epithelial cell surface, which is achieved through the cooperative action of epithelial cells, mucus, IgA, antimicrobial peptides and immune cells. 96Antimicrobial peptides produced by intestinal epithelial cells exert antimicrobial effects, including an enzymatic attack on the bacterial cell wall and the rupture of the bacterial inner membrane. 97One of the most characteristic mucosal antimicrobial peptides is RegIIIγ, the production of which in a MyD88-dependent way is carefully regulated by the flora. 98Indirectly, microbiota affects intestinal epithelial cells through cytokine generation by innate and adaptive immune cells in response to microbial colonization. 99

| Regulation of innate immunocytes by the microbiota
Antigen-presenting cells are regulated by microorganisms.The ubiquitous bacterial fermentation products SCFA is capable of activating G protein-coupled receptors on epithelial and hematopoietic cells and inhibiting histone deacetylase (HDACs). 83Elevation of circulating SCFA led to the generation of macrophage and dendritic cell (DC) precursors, followed by DCs with a high phagocytic capacity populating the lungs. 100SCFA can also change macrophages in the area by influencing their gene expression profile. 86In addition, microbiota also controls the homeostatic replenishment of monocytederived macrophages in the intestinal mucosa. 101hrough TLR signaling, microbial molecules such as lipopolysaccharides maintained steady-state production of neutrophils and primed neutrophils against bacterial infections. 102The microbiota also affects the number of innate cells like basophils that circulate through the bloodstream. 103On the other hand, stimulation of neutrophil function via microbiota proves to promote neutrophil "aging" through tonic sensing of TLR ligands. 104

| Regulation of nonclassical lymphocytes by the microbiota
It has been demonstrated that nonclassical lymphocytes, such as ILC, MAITs, NKT, and NK cells, are enriched at barrier sites during early life and can coordinate the interaction between the host and its microbiota.
ILC can produce IL-22, which can help keep some of the microbiota in the mucosal lymphoid structures, like Alcaligenes bacteria, under control. 105Recent evidence supports the idea that defined commensals may preferentially impact ILC3, the most noteworthy subset of ILC, but the mechanism remains unclear.As an illustration, SFB colonization can increase ILC3's ability to produce IL-22 in an IL-23-dependent manner. 106δT cells can be activated by TCR-mediated responses as well as responses to cytokines such as IL-1 and IL-23, 107,108 both of which can be promoted by the microbiota's action on tissues.][111] Nonclassical MHC molecules can present microbiota antigens with particular chemical modifications or amino acid motifs, thus making them possible to recognize microbiota-derived antigens or metabolites.In evolutionary terms, MAIT cells are limited by the nonpolymorphic and highly conserved MHC-Ib molecule, MHC class I-related protein 1 (MR1), 112 and are highly responsive to bacterial owing to their capacity to identify metabolic intermediates of the microbial riboflavin synthesis pathway. 113In addition, the growth of MAIT cells depends on the microbiota, as they are absent in aseptic mice. 114hen CD1d, an MHC class I-like molecule, is present, NKT cells respond to lipid antigens from both host cells and microbes.The accumulation of NKT cells in the colonic lamina propria is restricted by commensal colonization in early life. 914 | Regulation of T cell response by the microbiota CD4 + T cells, most of which are effector or memory T cells in the intestinal LP, respond greatly differently based on the different niches of colonization, antigen type, and metabolic property of gut microbiota.Upon activation by microbiota and presentation of antigens by APCs, CD4 + T cells generate distinct subsets and the functional plasticity of specific T cell subsets, 115 among which are Tregs and various T helpers (Th1) cells such as IFN-γ, IL-4, B cell regulating, and IL-17 producing Th1, Th2, Tfh, and Th17 cells.116,117 SCFAs from the gut microbiota have been shown to modulate T cell differentiation depending on their concentration and the surrounding immune environment.118 Th17 is crucial for host defense against external infections because of its ability to make IL-17.Th17 cell frequencies within the GALT of germ-free mice are significantly decreased.119 The colonization of commensal microbiota, particularly Clostridia-related segmented filamentous bacteria(SFB), has been shown to strongly stimulate the formation of Th17 cells in the small intestine.120 SFB promotes CD4 + T cell differentiation into RORγt-expressing Th17 cells via inducing the expression and release of serum amyloid A (SAA) from intestinal epithelial cells (IECs), which stimulates IL-22 production by increasing IL-1 and IL-23 in CX3CR1+ phagocytes.RORgt+ CD4 + T cells' IL-17 production can be upregulated by IL-22 because of its ability to boost SAA-mediated IL-1 production by phagocytes.106,121 The makeup of intestinal microbiota has a major impact on the repertoire of regulatory T cells (Tregs) that express the forkhead box P3 transcription factor (Foxp3-).122 Symbiotic bacteria, such as Clostridia strains cocktail and Bacteroides fragilis, were identified to possess Treg-inducing activity as well as the production of IL-10.123 In addition, SCFAs, particularly butyrate, have demonstrated to influence the formation and activity of regulatory T cells in the colon via enhancing acetylation of the Foxp3 locus in Tregs 90,124 and promoting TGFβ production, which indirectly contributes to the development of colonic Tregs.121 Moreover, the expression of transcription factor RORγt+ of RORγt+ Tregs, which are a separate group of Tregs in the colon, is induced by gut microbiota.125 Germinal centers (GCs) have been found to be the sites where high-affinity antibodies are produced, and Tfh has been found to be the primary cell subpopulation responsible for controlling B cells in these GCs.Transforming growth factor development is impaired in GF animals, however using a Toll-like receptor 2 (TLR2) agonist to activate intrinsic MyD88 signaling rescues this defect.126 Extracellular ATP (eATP), an important signaling molecule derive from microbiota, can restrict Tfh cell formation and GC reaction in the PPs by means of P2X7, regulate Tfh cell abundance, and influence the high-affinity sIgA response against intestinal colonization bacteria, which leads to enteropathogenic infection.127,128

| Regulation of B cell immune response by the microbiota
IgA is the most abundant isotype of antibodies and is essential in promoting early interactions with the microbiota and preserving microbial diversity and compartmentalization. 129 The production of intestinal IgA is greatly influenced by the microbiota because, physically, they are very close. 130It is possible for secretory IgA to be generated in either a T-independent (TI-IgA) or T-cell-dependent (TD-IgA) fashion (referred to as ID-IgA).
A fraction of antimicrobial polyreactive IgA in the gastrointestinal tract is produced via the high-capacity, low-affinity T-cell-independent passage. 131,1324][135] SFB potently promotes TI-IgA production by stimulating the postnatal development of isolated lymphoid tissues and tertiary lymphoid tissue in the gastrointestinal tract. 130,131evertheless, the majority of intestinal IgA, especially that directed against bacterial protein antigens, is T-cell reliant and a component of a low-capacity, high-affinity route. 131,132For PP subepithelial B cells to produce TD-IgA, affinity mature, and undergo class switch recombination, they must engage with antigen-loaded dendritic cells in a CCR6-dependent way. 44,136Bacteria such as SFB and Mucispirillum sp. can induce the production of TD-IgA, which may be due to enhancing acquisition of their antigens by DCs and supporting the growth of T helper 17 and T helper 1 cells in the gut. 132t is not just intestinal IgA that binds gut bacteria, but also certain subclasses of IgG and IgE, most of which are triggered via a T-cell-independent pathway. 137Wide range of microbes encounter at mucosal sites downregulates IgE to baseline levels while triggering the IgA isotype switch.IgE production is influenced by the gut microbiota via a pathway opposite to gut microbiotaregulated IgA response.Without microbial exposure, active CD4 + T cell-dependent B cell isotype switches to IgE at PPs, thus producing high levels of IgE. 138IgG that may identify bacterial surface antigens, such as murein lipoprotein (MLP), which are expressed on certain Gramnegative pathogens, can be decreased under homeostatic settings by selective Gram-negative gut symbionts. 121

| DISEASE AND TREATMENTS: NEIGHBORHOOD CONFLICTS ERUPT FROM TIME TO TIME
Under normal circumstances, the host and its microbiota endure mutualistic partnerships to achieve and maintain homeostasis.Nevertheless, when the dynamic crosstalk between the two goes amiss due to disorders of the microbiota or the host, dysbiosis will ensue.Studies have confirmed the role of an altered microbiome in human disorders and diseases (Table 2).

| Inflammatory bowel disease (IBD)
Immune recognition of gut microbiota triggers multiple inflammatory disorders, among which IBD is the most representative and well-researched.IBD encompasses primarily ulcerative colitis (UC), which is characterized by bloody mucous diarrhea, and Crohn's disease (CD), the hallmark of which is abdominal pain. 147Several laboratory and clinical studies have demonstrated that gut microbiota is a major driver of pathogenic inflammation.(Figure4).
The intestinal mucus layer shields the host epithelium from intestinal contents as the first line of defense.The mucus layer contains bacteria and dietary proteins, peptides, and IBD is characterized by a breakdown in the intestinal mucosal barrier. 148,149Recent research lends credence to the idea that a weakened colonic mucus barrier contributes to the etiology of UC.Specifically, a significant decrease in the structural MUC2 protein was detected in the colonic mucus of UC patients. 150oreover, in ulcerative colitis, a particular malfunction of the intestinal mucus layer has been noted.Defective glycosylation that allows bacteria to penetrate the otherwise impenetrable inner colonic mucus layer has been observed in UC patients and mouse models. 151An intricate protein complex, TJs, which regulates the paracellular gap and permeability, is responsible for determining the paracellular barrier function of the intestinal epithelium.In IBD intestinal tract, the continuous, linear chain pattern typical of TJs in epithelia changes to a granular appearance with strand breaks and loss of continuity, and fewer strands are horizontally aligned. 152,153anniculocyte defensins and Panniculocyte alterations also contribute significantly to Crohn's disease.A study found that Paneth cells from IBD patients overexpress NOD2.154 Expression of alpha-defensin HD5 and HD6 mRNAs and proteins reduced in the small intestine of Paneth cells from UC patients.Paneth cells, which are usually rare in the colon, may be found in the inflamed IBD colon, expressing α-defensins HD5 and HD6 as well as lysozyme and sPLA2.155,156 In contrast, Low PPARregulated HBD1 and impaired HBD2 and HBD3 induction characterize CD. 157,158 Clinical observations can indirectly demonstrate the major role of microbial communities. Forexample, in humans, the first evidence implicating gut microbiota in the etiology of IBD is that CD can be improved by surgical repair to redirect fecal flow 159 and increasing mucosal-associated bacteria in the nonterminal ileum after ileocecal resection for CD may trigger postoperative recurrence in patients.160 Furthermore, antibiotics, such as metronidazole, ciprofloxacin, or rifaximin, advantage in the management of inflammatory bowel disease.161,162 Due to these intricate and strong arguments, there is currently little doubt regarding the involvement of bacteria in disease initiation.
T A B L E 2 Microbial metabolites or components that are implicated in disease.

Inflammatory bowel disease
SCFAs [139]   B vitamins [89]   Compound K [89]   AHR ligands [140]   Colorectal cancer SCFAs [89,  141]   B vitamins [89]   N1,N12diacetylspermine [141,  142]   Bacterial vaginosis and other sexually transmitted infections Polyamines [143]   Obesity and metabolic syndrome TAMO [144]   SCFAs [145]   Infectious colitis (Clostridium difficile) Bile acids [146]  Metabolomic and metagenomics investigations have shown that active IBD patients have a notable imbalance in their microbial composition.There is a reduction in the population of helpful bacteria, specifically those belonging to the groups Bacteroidetes, Firmicutes, and Lachnospiraceae (Clostridia cluster IV and XIVa).Additional research has also demonstrated a reduction in the presence of the bacteria species Roseburia hominis and Faecalibacterium prausnitzii, which are known to produce butyrate. 163Faecalibacterium species have the ability to promote the production of anti-inflammatory cytokines, including IL-10, which leads to a reduction in pro-inflammatory cytokines in patients with inflammatory bowel disease (IBD). 164UC and ileal CD have been associated with a reduction in Faecalibacterium prausnitzii.Notably, the normalization of F. prausnitzii happened after UC patients achieved clinical remission. 165Research has also shown a substantial rise in the prevalence of detrimental Firmicutes species, Fusbacterium species, and Proteobacteria strains among patients with inflammatory bowel disease (IBD).The presence of adherent and invasive bacteria belonging to the facultative anaerobes genus Enterobacteriaceae, such as adherent-invasive Escherichia coli and other Fusobacterium species, is much higher in individuals with ileal CD and UC. 166urthermore, there is growing data indicating that viruses can stimulate both the innate and adaptive immune responses at the epithelial gut barrier, alongside bacteria.This viral activity also plays a role in the development of inflammatory bowel disease (IBD).Other studies have shown that there is an increase in the abundance of Caudovirales phages, Anellovirus, enteroviruses, Norovirus, and other eukaryotic viruses in CD and UC. 1678][169] These phages establish communication with immune cells by infecting the bacteria and triggering the production of IFNs and Th1 cell-mediated responses.IFNs are a class of cytokines that engage with the antiviral genes of the host.Cytokines have the ability to decrease the amount of virus present and regulate the reactions of macrophages. 170This connection creates a beneficial symbiotic environment for the virus to thrive within the host.
The new SARS-CoV2 virus, which causes COVID-19 infection, has the ability to trigger significant inflammation in the lungs and lead to gastrointestinal symptoms. 171,172COVID-19 receptor ACE2 expression is elevated in the intestinal epithelial cells of both UC and CD patients, regardless of the intensity of inflammation, in the terminal ileum and colon, as compared to control.Additional research is required to elucidate the mechanisms by which SARS-CoV2 specifically affects the immunological pathways and impacts the progression and treatment of inflammatory bowel disease (IBD) in individuals. 173

| Colorectal cancer (CRC)
Colorectal cancer (CRC) is one of the most prevalent tumorswith established etiology of molecular, genetic, and environmental mechanisms.It globally accounts for about 10% and has the third highest incidence and mortality rate of all cancers. 174There is emerging evidence that pathogenesis of CRC is strongly influenced by microorganisms in the surrounding environment.
Dysbiosis, which represents a compositional change of resident gut microbiota, is typical in both fecal and mucosal samples of CRC patients.Metagenomic studies suggested that the abundance of Fusobacterium, Porphyromonas, Peptostreptococcus, and Prevotella, as well as altered fungi (mycobiota), has increased. 175Metagenomic and metabolomic analyses have shown consistent associations of the onset and progression of CRC with specific bacteria, such as Fusobacterium nucleatum, and several microbial metabolites. 176,177Of particular interest to propose is the role of uncommon fungi, viruses, and archaea in colon cancer.The virome changes in patients with CRC: Betabaculus virus, Epsilon15likevirus, Mulikevirus, and Punalikevirus increased abundance, associated with increased severity and mortality.Colon eukaryotic viruses are capable of altering immunological homeostasis and inducing DNA changes via viraldependent pathways. 178It was observed that Malasseziomycetes enriched and Saccharomycetes lessened, and disturbance in the distribution of certain strains such as Aspergillus and Malassezia in CRC patients. 179It has also been reported that in mice, antifungal treatment aggravated CRC. 180Research on the relationship between archaea and CRC is still in its infancy, but it has been shown that CRC patients have more salt-loving and less methanogenic archaea. 181olorectal carcinogenesis is an intricate process.The following three mechanisms are most closely associated with mucosal immunity.
(1) CRC has the traits of long-standing chronic inflammation in the mucosa, which is also a distinctive feature of IBD; thus, the immunological factors affecting IBD enteropathy described above can also affect CRC.
(2) The NF-κB pathway in the mucosal epithelial cell is essential in controlling inflammation in cancer.
Target genes of the NF-κ B pathway encode proinflammatory cytokines (e.g., TNF-α, IL-1, and IL-6), chemokines (IL-8), and enzymes (COX-2) that are associated with tumor progression, survival, proliferation, and invasion. 182TNF-α promotes tumorigenesis by inducing reactive oxygen species (ROS) production and promoting DNA damage. 183COX-2 and IL-8 can stimulate tumor progression and invasion by promoting angiogenesis. 1843) The growth and spread of CRC is aided by Th17 cells and IL17.Laboratory detection of human CRC specimens found most colorectal tumors contain Th17 cells. 185In addition, altered expression profiles of genes in Th17 cells lead to a shorter disease-free survival time in CRC patients. 186olorectal tumor stroma showed elevated levels of IL17A, which induces stromal production of factors that maintain tumor cell proliferation, survival, and angiogenesis. 1874) Recently the role of innate systems, particularly innate lymphocytes (ILC), has been highlighted the in the pathogenesis of CRC.Intestinal ILCs drive both pro-and antitumor actions, tilting the scales in favor of tumor formation.The activation of ILC3 and the subsequent generation of cytokines appear to be crucial to their effect on colorectal cancer.The expression of IL-23 is higher in human colon cancers than in healthy tissue, and it is associated with a worse prognosis and more aggressive disease.188 There are preventive and pathogenic functions for the ILC3-driven IL-22 pathway in colitis and cancer, respectively.By activating a DNA damage response pathway, IL-22 shields the gut from the effects of genotoxic stress.When enterocytes are exposed to carcinogens, the loss of IL-22 or IL-22 receptors on epithelial cells causes a delay in tissue healing, increased inflammation, and tumor growth.189,190

| Mucosal vaccine
Vaccines could have a significant bearing on preventing the spread of disease even beyond the individual who receives them on the premise of extensive coverage. 191However, conventional vaccinations are given via systemic means, meaning they are injected with a syringe and needle.This approach typically results in minimal or nonexistent antigenspecific immune responses at mucosal surfaces. 1924][195] Mucosal vaccines are preferable to injectable vaccinations not only because they are more effective immunologically, but also because they have a number of advantages from a production and regulatory perspective: (1) can be self-administered, not requiring trained health professionals for administration and greatly decreasing the cost of mass immunization；(2) eliminating needleassociated risks and cause less physical and psychological discomfort; (3) not following strict sterile procedures thus simplifying production and storage. 196e have a range of licensed vaccines proving the viability of oral immunization. 197It has been demonstrated that oral vaccines can generate mucosal IgA and serum IgG, as well as memory T cells and synergistic effectors in the gastrointestinal tract and salivary and mammary glands. 198Currently licensed vaccines include the oral polio vaccine (OPV), which was the first successful mucosal vaccine developed; live oral typhoid vaccine (Ty21a); cholera vaccine; rotavirus vaccine; and oral adenovirus vaccine. 199everal bacterial shuttle vector systems have then been tested for use as mucosal vectors.From 2015 to the present, bacteria used as mucosal vects include Salmonella spp., Listeria spp., Bacillus spp.Lactococcus and other novel bacterial vectors.Listeria and Salmonella have been extensively employed as vaccine vectors in several diseases, including cancer immunotherapy. 200owever, It is important to consider the safety concerns associated with using live-attenuated pathogenic bacteria as a recombinant delivery method.These bacteria have the potential to revert back to their pathogenic state, thus more research is needed. 201Consequently, researchers have investigated commensal bacteria to enhance safety without compromising effectiveness or altering the immunological response they elicit.Some of these commensal bacteria tested include Bacillus spores, such as Bacillus subtilis (B.subtilis).These microorganisms have been utilized as a live vaccine vector system because of their safety, vitality, secretory capacity, and probiotic traits.B. subtilis has been employed in numerous research investigations as a vehicle for vaccines targeting viruses, harmful bacteria, and parasites in animal models. 202In addition, Oh and co-workers 203 used B. subtilis spores to express the protective antigen (PA) derived from Bacillus anthracis and evaluating the effectiveness of the construct in inducing an immune response in mice through various administration routes.Their research found that regardless of how the medication was given, the mice showed higher levels of active antibody titer, isotype profiles, toxin-neutralizing antibody in their blood, and IgA in their saliva.
Lactobacilli, a potential commensal candidate, is being produced with a strong tolerance to acid and bile stress.It exhibits survival times exceeding 7 days.
Lactobacilli have recently been proposed as a potential enhancer for several vaccine designs, showing the ability to modify both the innate and adaptive immune responses in clinical trials, particularly in gastroenterological conditions including rotavirus, cholera, and Salmonella infection, 204 and additionally for respiratory infections such as Influenza, SARS-CoV-1, pneumonia, and Bacillus anthracis and so on. 204he components and metabolites of microbiota may impact vaccine effectiveness and adjuvant action.The gut microbiota of people from industrialized and poor nations is distinguished, and studies on vaccine efficacy vary among regions. 205People living in underdeveloped countries with poor sanitation have weakened immune responses to oral vaccines such as rotavirus, 206 poliovirus, 207 and cholera vaccines 208 in Nicaragua. 209Even in the same country, Indian children in poorer regions showed reduced mucosal immune responses after vaccination with monovalent and trivalent oral poliovirus vaccine. 210As a matter of fact, an abundance of stool Actinobacteria was shown to be positively correlated with higher responses to oral and parenteral vaccines; nevertheless, Clostridiales, Enterobacteriales, and Pseudomonadales were related to lower vaccine responses. 211Animal studies provide further evidence that microbiota make up of one's digestive tract affects the efficacy of vaccines via mediating antibody responses.Mice treated with clarithromycin or doxycycline decreased in the production of induced antibodies after rejecting the hepatitis B virus surface antigen (HBsAg) vaccine.At the same time, enhanced immune responses to live attenuated Salmonella enterica serovar Typhi (Ty21a) vaccine. 212Furthermore, research proves that Correlations between Oscillospira and Streptococcus and the induction and protection of vaccine-specific IgG and IgA were positive and negative, respectively. 213t is impossible to augment and direct a highly vaccine-specific adaptive immune response without the use of mucosal adjuvants.Due to the powerful immunostimulatory capacity of bacterial-derived components, they are a major source of possible adjuvants.For example, lipopolysaccharide (LPS), peptidoglycan (PGN), CpG DNA, and trehalose dimycolate (TDM) can strengthen the immune response against antigens through the activating TLRs, NLRs, and CLRs (C-type lectin receptors). 214Mice lacking the TLR5, the specific receptor specific for bacterial flagellin, generated substantially fewer antibodies after receiving the trivalent inactivated vaccine (TIV) than normal mice.This result manifests that flagellin from the gut microbiota can act as an adjuvant to increase antigen responses to the TIV vaccine. 215

| CONCLUSIONS
A sophisticated system that is essential to maintaining good health is the mucosal immune system.The gastrointestinal microbiome, the largest symbiotic ecosystem with the host, is an essential contributor to maintaining intestinal homeostasis.The intestinal innate and adaptive immunity tolerate symbiotic microbiota and retain the ability to exert a pro-inflammatory response towards invasive pathogens.When this balanced relationship is disrupted, ecological dysregulation and intestinal immune abnormalities develop, leading to microbiota dysbiosis, compromised integrity of the intestinal barrier, and pro-inflammatory immune responses towards symbionts.Recent data has shown the fundamental relationship between the gut microbial environment and gastrointestinal disorders, and this presents a huge therapeutic opportunity for health promotion and disease management.
Recent accumulating evidence has revealed complex interactions between the gut microbiota and host cells in the gut ecosystem; nevertheless, there are still unresolved matters about undiscovered bioactive microbial metabolites and the interplay of gut microbes, encompassing bacteria, fungi, viruses, and other microorganisms.Advanced techniques such as metagenomics, metatranscriptomics, and metabolomics will provide new information about the functional properties of the microbiome and host cells in both healthy and diseased states.These strategies will enhance our comprehension of the internal mechanisms of the gut ecosystem and the various constituent elements involved.These potent instruments have been discerning the connection between gut microbial metabolites and systemic ailments, such as neurological disorders and cardiovascular conditions.Additional research involving thorough analysis of human samples, biological tests, and animal experiments.

T A B L E 1
Microbial colonization of the GI tract.

F I G U R E 2
Mucosal immune response against pathogenic microbial infections.① TLR from innate immunity recognizes dysregulated microbiota and leads to the initiation of NF-κB-dependent downstream spindle inflammation positive runners.The NF-κB signaling cascade can also be activated by microbial derivatives.② Gut bacteria can also transmit to the gut lumen and are sampled by DCs.③ DCs create a tolerogenic response by stimulating Treg cells to secrete IL-10, which in turn induces a tolerogenic response.Pathogens activate macrophages and DCs, which stimulates several subpopulations of T cells, including Th17and ILC3s, among others, secrete IL-17 and IL-22.④ These cell subsets stimulate the intestinal epithelium to release neutrophil-attracting CXC chemokines, hence enhancing the host response.⑤Secreted lgA from plasma cells can also regulate microbiota and pathogens.

F I G U R E 4
Immune response in IBD.Genetic and environmental variables affect the composition of the intestinal microbiota, which plays a protective role in normal hosts but contains an unbalanced ratio of helpful and aggressive bacterial species (dysbiosis) in inflammatory bowel disease (IBD).To put it simply, antimicrobial proteins, such as REG3γ, are induced under healthy conditions (left panel) and pathogens are kept in check as a result to maintain equilibrium.In IBD (right panel), hyperactivation of T Th1 and Th17 cells, increased permeability of tight junctions, decreased regulatory Treg cells, and decreased REG3 and IL-10 are all results of chronic inflammation that is allowed to run amok.